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Vol 15: Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots.This article is from BMC Bioinformatics, volume 15.AbstractBackground: Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. Results: This work proposes a new method, βACVASA, to predict the change of binding free energy after alanine mutations. βACVASA integrates accessible surface area ASA and our newly defined β contacts together into an atomic contact vector ACV. A β contact between two atoms is a direct contact without being interrupted by any other atom between them. A β contact’s potential contribution to protein binding is also supposed to be inversely proportional to its ASA to follow the water exclusion hypothesis of binding hot spots. Tested on a dataset of 396 alanine mutations, our method is found to be superior in classification performance to many other methods, including Robetta, FoldX, HotPOINT, an ACV method of β contacts without ASA integration, and ACVASA methods similar to βACVASA but based on distance-cutoff contacts. Based on our data analysis and results, we can draw conclusions that: i our method is powerful in the prediction of binding free energy change after alanine mutation; ii β contacts are better than distance-cutoff contacts for modeling the well-organized protein-binding interfaces; iii β contacts usually are only a small fraction number of the distance-based contacts; and iv water exclusion is a necessary condition for a residue to become a binding hot spot. Conclusions: βACVASA is designed using the advantages of both β contacts and water exclusion. It is an excellent tool to predict binding free energy changes and binding hot spots after alanine mutation.